Thanks for your comments.
You've definitely identified one of the reasons why supporting this request is quite difficult
Part of the problem lies in identifying which mappings are legitimate and which are not.
Supporting one-to-many compares and syncs is a feature that is often requested for our SQL Compare tool - I've created a feature request for this in Schema Compare so we can track how popular it is with our users.
It's definitely something we'd really like to do, but unfortunately would require a significant amount of rework to the engine.